Alberto Santos Zavaleta

Computational Genomics Support staff

UNAM

Academic history

Links

Scopus

Telephone: (777) 3132063
Email: asantos@ccg.unam.mx

Publications

YearPublicationPMID
2019Santos-Zavaleta, A, Salgado, H, Gama-Castro, S, Sánchez-Pérez, M, Gómez-Romero, L, Ledezma-Tejeida, D, García-Sotelo, J, Alquicira-Hernández, K, Muñiz-Rascado, L, Peña-Loredo, P, Ishida-Gutiérrez, C, Velázquez-Ramírez, D, Del Moral-Chávez, V, Bonavides-Martínez, C, Méndez-Cruz, C, Galagan, J, Collado-Vides, J. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2017Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD. (2017). "The EcoCyc database: Reflecting new knowledge about Escherichia coli K-12". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003]27899573
2016Gama-Castro, S, Salgado, H, Santos-Zavaleta, A, Ledezma-Tejeida, D, Muñiz-Rascado, L, García-Sotelo, J, Alquicira-Hernández, K, Martínez-Flores, I, Pannier, L, Castro-Mondragón, J, Medina-Rivera, A, Solano-Lira, H, Bonavides-Martínez, C, Pérez-Rueda, E, Alquicira-Hernández, S, Porrón-Sotelo, L, López-Fuentes, A, Hernández-Koutoucheva, A, Del Moral-Chavez, V, Rinaldi, F, Collado-Vides, J. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156]26527724
2014Gama Castro, M, Rinaldi, F, López Fuentes, A, Balderas MartÍnez, Y, Clematide, S, Ellendorff, T, Santos Zavaleta, A, Marques-Madeira, H, Collado Vides, P. (2014). "Assisted curation of regulatory interactions and growth conditions of OxyR in E. Colik-12". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2014():bau049-. [doi:10.1093/database/bau049]24903516
2013Weiss, V, Medina-Rivera, A, Huerta, A, Santos-Zavaleta, A, Salgado, H, Morett, E, Collado-Vides, J. (2013). "Evidence classification of high-throughput protocols and confidence integration in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2013():bas059-. [doi:10.1093/database/bas059]23327937
2013Salgado Osorio, H, Peralta Gil, M, Gama Castro, M, Santos Zavaleta, A, Muñíz Rascado, L, Garcia Sotelo, J, Weiss, V, Solano Lira, H, Martínez Flores, I, Medina Rivera, A, Salgado Osorio, G, Alquicira Hernández, S, Alquicira Hernández, K, López Fuentes, A, Porrón Sotelo, L, Huerta Moreno, A, Bonavides Martínez, C, Balderas MartÍnez, Y, Pannier, L, Olvera, M, Labastida, A, Jiménez-Jacinto, V, Vega-Alvarado, L, del Moral Chávez, V, Hernández Álvarez, A, Morett, E, Collado Vides, P. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201]23203884
2013Keseler, I, Mackie, A, Peralta Gil, M, Santos Zavaleta, A, Gama Castro, M, Bonavides Martínez, C, Fulcher, C, Huerta Moreno, A, Kothari, A, Krummenacker, M, Latendresse, M, Muñíz Rascado, L, Ong, Q, Paley, S, Schroder, I, Shearer, A, Subhraveti, P, Travers, M, Weerasinghe, D, Weiss, V, Collado Vides, P, Gunsalus, R, Paulsen, I, Karp, P. (2013). "EcoCyc: Fusing model organism databases with systems biology". Nucleic Acids Research. 41(D1):605-612. [doi:10.1093/nar/gks1027]23143106
2011Santos Zavaleta, A, Gama Castro, M, Pérez Rueda, E. (2011). "A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins". MICROBIOLOGY-SGM. 157(5):1393-1401. [doi:10.1099/mic.0.042937-0]21310789
2011Keseler, I, Collado Vides, P, Santos Zavaleta, A, Peralta Gil, M, Gama Castro, M, Muñíz Rascado, L, Bonavides Martínez, C, Paley, S, Krummenacker, M, Altman, T, Spaulding, A, Spaulding, A, Pacheco, J, Latendresse, M, Fulcher, C, Sarker, M, Shearer, A, Mackie, A, Paulsen, I, Gunsalus, R, Karp, P. (2011). "EcoCyc: A comprehensive database of Escherichia coli biology". Nucleic Acids Research. 39(SUPPL. 1):583-590. [doi:10.1093/nar/gkq1143]21097882
2011Gama Castro, M, Salgado Osorio, H, Peralta Gil, M, Santos Zavaleta, A, Muñíz Rascado, L, Solano Lira, H, Jimenez-Jacinto, V, Weiss, V, Garcia Sotelo, J, López Fuentes, A, Porrón Sotelo, L, Alquicira Hernández, S, Medina Rivera, A, Martínez Flores, I, Alquicira Hernández, K, Martínez Adame, R, Bonavides Martínez, C, Miranda-Ríos, J, Huerta Moreno, A, Mendoza-Vargas, A, Collado Torres, L, Taboada, B, Vega-Alvarado, L, Olvera, M, Olvera, L, Grande, R, Morett, E, Collado Vides, P. (2011). "RegulonDB version 7.0: Transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)". Nucleic Acids Research. 39(SUPPL. 1):98-105. [doi:10.1093/nar/gkq1110]21051347
2009Keseler, I, Bonavides-Martinez, C, Collado-Vides, J, Gama-Castro, S, Gunsalus, R, Johnson, D, Krummenacker, M, Nolan, L, Paley, S, Paulsen, I, Peralta-Gil, M, Santos-Zavaleta, A, Glennon Shearer, A, Karp, P. (2009). "EcoCyc: A comprehensive view of Escherichia coli biology". Nucleic Acids Research. 37(SUPPL. 1):464-470. [doi:10.1093/nar/gkn751]18974181
2009Collado-Vides, J, Salgado, H, Morett, E, Gama-Castro, S, Jimenez-Jacinto, V, Martinez-Flores, I, Medina-Rivera, A, Muniz-Rascado, L, Peralta-Gil, M, Santos-Zavaleta, A. (2009). "Bioinformatics resources for the study of gene regulation in bacteria". Journal Of Bacteriology. 91(1):23-31. [doi:10.1128/JB.01017-08]18978060
2008Gama Castro, M, Jiménez Jacinto, V, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Contreras Moreira, B, Segura Salazar, J, Muñíz Rascado, L, Martínez Flores, I, Salgado Osorio, H, Bonavides Martínez, C, Abreu Goodger, C, Rodríguez Penagos, C, Miranda-Ríos, J, Morett Sánchez, J, Merino, E, Huerta Moreno, A, Treviño Quintanilla, L, Collado Vides, P. (2008). "RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation". Nucleic Acids Research. 36(SUPPL. 1):120-124. [doi:10.1093/nar/gkm994]18158297
2007Karp, P, Keseler, I, Shearer, A, Latendresse, M, Krummenacker, M, Paley, S, Paulsen, I, Collado Vides, P, Gama Castro, M, Peralta Gil, M, Santos Zavaleta, A, Peñaloza Spinola, M, Bonavides Martínez, C, Ingraham, J. (2007). "Multidimensional annotation of the Escherichia coli K-12 genome". Nucleic Acids Research. 35(22):7577-7590. [doi:10.1093/nar/gkm740]17940092
2006Salgado Osorio, H, Santos Zavaleta, A, Gama Castro, M, Peralta Gil, M, Peñaloza Spinola, M, Martínez Antonio, A, Karp, P, Collado Vides, P. (2006). "The comprehensive updated regulatory network of Escherichia coli K-12". Bmc Bioinformatics. 7():5-5. [doi:10.1186/1471-2105-7-5]16398937
2006Salgado Osorio, H, Gama Castro, M, Peralta Gil, M, Díaz Peredo, E, Sánchez Solano, E, Santos Zavaleta, A, Martínez Flores, I, Jiménez Jacinto, V, Bonavides Martínez, C, Segura Salazar, J, Martínez Antonio, A, Collado Vides, P. (2006). "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.". Nucleic Acids Research. 34(Database issue):394-397. [doi:10.1093/nar/gkj156]16381895
2004Salgado Osorio, H, Gama Castro, M, Martínez Antonio, A, Díaz Peredo, E, Sánchez Solano, E, Peralta Gil, M, García Alonso, D, Jiménez Jacinto, V, Santos Zavaleta, A, Bonavides Martínez, C, Collado Vides, P. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140]14681419
2001Hershberg, R, Bejerano, G, Santos-Zavaleta, A, Margalit, H. (2001). "PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites". Nucleic Acids Research. 29(1):277-277. [doi:10.1093/nar/29.1.277]11125111
2001Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martinez, C, Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 29(1):72-74. [doi:10.1093/nar/29.1.72]11125053
2000Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, F, Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 28(1):65-67. [doi:10.1093/nar/28.1.65]10592182
2018Santos-Zavaleta, A, Sanchez-Perez, M, Salgado, H, Velazquez-Ramirez, D, Gama-Castro, S, Tierrafria, V, Busby, S, Aquino, P, Fang, X, Palsson, B, Galagan, J, Collado-Vides, J. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOL. 16(1):91-91. [doi:10.1186/s12915-018-0555-y]30115066
2006Peñaloza Spinola, M, Peralta Gil, M, Gama Castro, M, Contreras Moreira, B, Santos Zavaleta, A, Martínez Flores, I, Collado Vides, P. (2006). "RegulonDB: Going beyond transcriptional regulation". Proceedings Of The Fifth International Conference On Bioinformatics Of Genome Regulation And Structure, Vol 3. ():322-322.